DNA migrates faster the longer you run a gel? - (Jan/22/2006 )

I'm wondering if anyone has also noticed that when you run an agarose gel with DNA. The DNA starts out migrating real slow, but the more you run the gel, the faster the DNA migrates!?

Actually I'm not sure if it's true, but...

It seems like it takes forever for the bromophenol blue dye to get 1/4 of the way through the gel, but takes far less time for the dye to get from, say, 1/2 to 3/4 of the way through.

Anyone know why?

Hi Neurospora,

Maybe what you are seeing is that DNA takes it's time getting out of the well... When DNA and bromophenol blue are out of it, it has no more obstacles...

Esther

Or is it that he gel is warming? The agarose is becoming a litlle looser and the DNA can migrate faster?

Of course it runs faster! Molecular weight vs distance migrated is not a linear relationship.

Have you noticed that the bands at the bottom of the gel on a DNA ladder that are of lower molecular weight are further spaced apart in the gel than the bands that are high molecular weight.

When I was an undergrad we did an exercise to determine the molecular weight more accurately of a particular unknown DNA fragment. We ran the unknown fragment next to a ladder of known molecular weight. From a picture of the gel, we determined the distance migrated for each of the bands in the known molecular weight ladder and plotted this relationship on 2-cycle semi-log paper where the distance traveled was on the x-axis. The molecular weight was plotted on the y-axis...the log portion. From a best fit line, the molecular weight of the unknown DNA fragment could be determined. If you plot this on straight linear graph paper, you'll need to take the log of the molecular weight first.

I believe what neurospora meant was that DNA from the same size will not migrate at the same speed (millimeters per minute) when the run starts versus when the run has been going on for quite some time... Of course smaller DNA runs faster that longer DNA, and the relationship is indeed not linear.

I've noticed the more rapid movement after some time of running a gel as well, and I noticed that this coincided with warming up of the TAE, as well as an increase of the current running through the gel (for the same voltage that is). Maybe indeed the agarose becomes more loose due to heating up?